MolNFT v1 · #11104 · protein
Crystal structure of human protein farnesyltransferase complexed with farnesyl diphosphate and the peptidomimetic inhibitor L-739,750
1JCQ · Protein farnesyltransferase, alpha subunit: “Crystal structure of human protein farnesyltransferase complexed with farnesyl diphosphate and the…”. X-ray diffraction, 5 ligands (FPP, 739, GLC), 10 pockets (best druggability 0.80).…
- PDB
- 1JCQ
- Type
- protein
- Length
- 723 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein farnesyltransferase, alpha subunit; Protein farnesyltransferase, beta subunit
- EC
- 2.5.1.-
- UniProt
- P49354, P49356
- Ligands
- FPP, 739, GLC, FRU, ZN
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein farnesyltransferase, alpha subunit (EC 2.5.1.-) | protein | 313 | 71% helix, 1% strand | P49354 |
| B | Protein farnesyltransferase, beta subunit (EC 2.5.1.-) | protein | 410 | 50% helix, 7% strand | P49356 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- 739 · 2(S)-{2(S)-[2(R)-amino-3-mercapto]propylamino-3(S)-methyl}pentyloxy-3-phenylpropionylmethionine sulfone · ligand · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- ZN · Zinc ion · metal · chains B
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.80 | 0.86 | 81 | empty |
| 2 | 960 | 0.76 | 0.79 | 66 | FPP, 739 |
| 3 | 223 | 0.62 | 0.82 | 27 | ACY |
| 4 | 155 | 0.45 | 0.76 | 25 | empty |
| 5 | 102 | 0.42 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3463 Ų buried · 74 hydrogen bonds · protein-protein
Compared structures
- 1JCQ · Crystal structure of human protein farnesyltransferase complexed with farnesyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P49356 · AlphaFold monomer V2.0 prediction for protein farnesyltransferase subunit beta (P49356) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P49354 · AlphaFold monomer V2.0 prediction for protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERAS… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P49354
- Every structure of UniProt P49356
- Elsewhere: RCSB PDB 1JCQ · PDBe 1JCQ · UniProt P49354 · UniProt P49356
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